28NM | pdb_000028nm

Crystal structure of the human galectin-1 in complex with p-Methoxyphenyl 3-O-benzyl-beta-D-galactopyranoside

PDB DOI: https://doi.org/10.2210/pdb28NM/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-02-09 Released: 2026-09-16
Deposition Author(s): Silvestri, I., Saviano, M.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.279 (Depositor), 0.279 (DCC)
R-Value Work:
0.228 (Depositor), 0.228 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 28NM

This is version 1.0 of the entry. See complete history.

Literature

Exploring the selectivity of molecules targeting the carbohydrate binding site in galectins

Silvestri, I., Filocaso, M., Capasso, D., Iadonisi, A., Di Gaetano, S., Pirone, L., Saviano, M., Pedone, E.M.

(2026) Sci Rep

DOI: https://doi.org/10.1038/s41598-026-69841-4

Macromolecule Content

Total Structure Weight: 29.75 kDa
Atom Count: 2,112
Modeled Residue Count: 268
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	A, B	137	Homo sapiens	Mutation(s): 0 Gene Names: LGALS1
UniProt & NIH Common Fund Data Resources
Find proteins for P09382 (Homo sapiens) Explore P09382 Go to UniProtKB: P09382
PHAROS: P09382 GTEx: ENSG00000100097
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09382
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.279 (Depositor), 0.279 (DCC)
R-Value Work: 0.228 (Depositor), 0.228 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.951	α = 90
b = 57.627	β = 90
c = 112.153	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union (EU)	European Union	--

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.